A Family Affair
by AllonsyJawn
Summary: The Sequel to Sunday tea. Sherlock is getting ready to tell John that he loves him when he gets some disturbing news. Jack Harkness's disappearance is only the beginning of a series of well laid plans meant to distract the detective - but from what? Two people are working to take over the world, and there's only one family that can stop them.
1. Chapter 1

**Hooray! I actually managed to start this one! Here it is, the sequel to Sunday Tea. Thanks as always guys, R and R, Enjoy!**

Sherlock sat at the kitchen table, pursing his lips at the infernal clock above the sink. As a child he'd found the slow, steady tick of a clock to be soothing. Time often moved out of order for him, and a steady metronome that ticked away the moments meant consistency to his otherwise hectic life. Nowadays, as an adult, he had grown to hate the sound. Instead of a ballast to cling to, the clock now meant he was a prisoner, doomed to live every second exactly when it was intended to be lived. Normally this wouldn't have bothered him enough to warrant the deadly glares he was sending towards the clock, but it was different today. Everything was different today.

It had been two weeks now since John Watson had discovered one of the deeply held secrets of his flatmate. He appeared, at least to Sherlock, to have become something akin to comfortable with the fact that he was living with a half alien. After that first night, Sherlock had been on edge for days, waiting for the other foot to drop. Any day, he'd thought, any day now John will realize the gravity of the situation. He'd be able to see it in his friends eyes when he realized what everyone else already knew- that the Holmes brothers were freaks. Every day he would sneak a furtive glance at John's face, but each time the dreadful word was not mirrored back to him.

Despite all common sense, John was willing to look past the secret of his birth and childhood. But there was another secret, something that couldn't be so easily swept beneath the rug. Sherlock wanted nothing more than to keep this final secret to his grave, and before the last visit by his parents that had been his intention. This was a delicate situation, and the truth needed to come from his own mouth. Time was running out though- his mother was threatening to come forward before he had a chance to. It was unavoidable. He had to tell John that he was in love with him.

It was almost time. He'd made this decision three days before-that he'd give himself the proper time to prepare, and then be obligated to tell John the truth an hour after he returned from work on Friday night. This was mostly based on things he had observed while living with the army doctor, with the goal being to catch him at the best possible time. John was always in a poor mood Sunday and Monday night, so those nights were not a possible option. Tuesdays he usually watched some little singing show whose name Sherlock repeatedly deleted from his mind whenever he accidently learned it. Wednesdays he updated his blog, and although he doubted his flatmate would be angry enough to immediately post about the incident, he didn't want to take the chance. Thursday was a plausible option, but if John needed time to process the information then he would be distracted at work the next day. Friday and Saturday were left, and he was more apt to have a drink as soon as he was home from the clinic Friday. The logic was sound, impeccably poured over, and sure to be his best bet. He was terrified.

His phone buzzed twice- his notification that someone had sent him an email. He rolled his eyes; he'd been ignoring some boring-looking cases since they'd had their trip in the blue box. There was no need to bother with simple cases when most of his brain power was focused on the task at hand.

He heard the key turn in the lock. Both of his hearts beat out an adrenal Symphony, but his face was composed and smooth. John came into the flat, unaware of his friend's intense distress.

"Sherlock," he asked, as he pulled off his coat, "why was the door locked?"

"A particularly boring client has been trying to visit. I heard him knocking like a maniac when I was trying to sleep earlier."

"Have you spoken to him?"

"No."

"Then how do you know he'll be boring?"

"Persistence like his only comes into practice when there's a love affair. Love affairs make for boring cases." Sherlock inwardly cringed once the words came out. _Yes, good idea, tell him what a bad idea love is now, you idiot._

John shrugged and locked the door behind him, flopping down in his red chair in front of the fireplace. Sherlock bit the inside of his lip and picked up the small brown bag he'd been hiding behind his feet. From inside he pulled a tall bottle of John's preferred beer and a small bag of red licorice. He walked casually over to John's chair and set the snacks on his stand before folding himself into his own chair across the rug from his friend.

John frowned at the small offering, raising a suspicious eyebrow. "Beer and licorice?"

"You prefer it to chocolate, correct?"

"Well, yeah, but why did you buy some?"

"I was already out."

"Doing what?"

"Shopping."

"You never shop."

"We were out of milk."

"So you bought milk then?"

"Nnnnnnno, I forgot the milk."

John looked him once up and down, sizing him up slowly. He leaned forward accusation swimming in his eyes. "Sherlock, is this poisoned?"

"What? No, why would I—"

"You've done it before."

"Oh, one time, John! And it turned out to only be sugar."

"Then why would you buy me beer and licorice?"

"Because we're friends, John! I'm allowed to do that, aren't I? Friends can buy each other something to nibble on after work. Or is that some great silent rule, like not telling someone they've gained weight but congratulating them when they lose it? Honestly I can't be expected to memorize all of these silly little human guidelines."

"Okay!" John said, quickly, holding up his hand. "Okay. Thank you." He opened the beer quickly, letting Sherlock see him take a sip to show he appreciated it. "Any interesting cases come around today? It's been a while."

"No, nothing important."

John winced. "Ouch. You must be going mad, cooped up in here with nothing exciting to do."

About twenty minutes passed. For any other two people, sitting in such heavy silence would have been awkward, but the two of them were used to just existing in each other's company.

"John," Sherlock finally started, taking a moment to steady himself. "There's something…we need to discuss something."

"What is it?"

_Do it quick, like a Band-Aid_. "I… Okay, last week when my parents were here—"

There was a loud knock on the door. "Mr. Holmes?" a deep voice called. Mr. Holmes, are you home?"

Sherlock sighed, rubbing a hand over his face as he dropped his voice to a whisper. "Oh, _God_. Ignore him, he'll go away. Anyway, John, I was talking to my mother, and she suggested that I tell you—"

The next knock at the door was much fiercer, and this time it was a woman's voice. With a thick welsh accent she hollered into the flat. "To hell with this! We don't have time to be chasing after you!"

There was a buzzing sound, a whining charge echoing through the flat.

John frowned. "What is that sound?"

Sherlock's eyes widened, then he dived across the rug and pulled John to the ground, covering both of their heads at the last possible minute. There was a loud explosion as the locked door burst into hundreds of small pieces, flying past their heads and scattering all across the room. Sherlock heard a window shatter somewhere and the sound of John's favorite teacup shattering on the coffee table.

Sherlock winced as his ears rang, automatically brushing a few light splinters out of John's hair before jerking his hand back. He'd never actually touched John's hair before, and he was struck by the soft, choppy feel of it. This was not the time.

Smoke settled and the two men peered up from the carpet as a man and woman walked through the smoking hole where their door had been.

"Jesus, Gwen!" the man said, rubbing his ears. "I thought you said it would just open the door!"

"It did," she shrugged, wincing a bit. In her hands was a large gun unlike anything John had ever seen.

The army doctor jumped to his feet, grabbing his hand gun from its hiding place underneath his armchair and pointing it back at the woman.

"Hey!" she said pointing the barrel of the weapon towards him. "Drop it!"

"I don't bloody think so!" John said, mouth hanging open in shock as he surveyed the damage. "Look at my door! Who the hell are you?"

"Are you Sherlock Holmes?" she asked skeptically. "I thought you'd be taller."

"John," Sherlock said quickly, "you can lower the gun. She can't hurt us."

"That…. That _thing_ she's holding just blew in our door!"

"It's a Sontaran Squareness gun. A malfunctioning, _old _model, but definitely Sontaran. She won't be able to shoot it again for at least a half hour while it recharges."

Gwen frowned, inspecting the weapon. The man next to her crossed his arms. "Really? That's a terrible idea for a weapon."

"It's not a weapon," Sherlock said angrily, stalking over and ripping the gun from Gwen's hands. "It's used for emergency exits. Only an ignorant, stupid life-form, playing with things beyond their base intelligences, would use it as a weapon. I am Sherlock Holmes, and you need to leave. Now."

My name is Ianto Jones, and this is Gwen Cooper," the man said holding out his hand. Sherlock just glared at him so he shrugged and put the hand back in his pocket. "You've been ignoring us, Mr. Holmes. Do you ever check your Email? We must have left a thousand messages, and I've been to your flat every day—"

"I'm aware," Sherlock snapped, turning on his heel. "If you're here so often, it should be easy for you to find your way home from here, yes?"

"Mr. Holmes—"

"I decide what cases I take on!" he said sharply as he walked away through the kitchen. "I thought my complete lack of reciprocity might be enough, but I guess I'll have to spell it out for you. I'm. Not. Interested. We'll be sending you the bill for the door. Now get out before we call the police."

"You will listen to what we have to say!" Gwen started, but Ianto held up his finger to her.

"Mr. Holmes, Captain Jack Harkness sent us here."

They heard Sherlock's footsteps stop, then he slowly walked back into the living room, fixing the suited man with a suspicious glare. "Jack Harkness has my mobile number. If he needed me, he would have called."

"He can't."

"Why not?"

"That's the point, Mr. Holmes. Jack is missing. Has been for almost two weeks. He left us protocols, instructions on what to do is he goes missing and doesn't contact us. There were places for us to check, contacts to ask about his whereabouts, but no one knows anything. At the top of the protocols, it says that if we can't find him, we find Mr. Sherlock Holmes at 221 B Baker Street."

Sherlock frowned, staring at the floor as the wheels in his head turned. "Who are you?"

"I told you—"

"To him. Who are you to Jack Harkness?"

"I'm…he's our boss," Ianto said.

Sherlock saw the slight tinting of his cheeks and remembered his father talking about Jack's special male interest of this century. "Any leads?"

John guffawed. "You're actually considering helping them? After they broke our flat?"

Sherlock sighed a bit guiltily. "Jack is family, John."

John's eyes widened. "Oh. Like…_ your_ family?"

"Sort of. If you don't want to get involved—"

"No," John said quickly. "I didn't know. I'll help."

Ianto pulled a small piece of paper out of his pocket and handed it to Sherlock. "This is our only clue. It was laying on top of Jack's desk the day he disappeared."

Sherlock took the paper, and almost immediately smirked. Across the little paper was a number.

_487879465327_

"We don't know what it means," Ianto said. "It's too long for a phone number, too short for proper coordinates—"

"I know what it is," Sherlock said, flipping the little strip over. His smile faded immediately. There, typed in small black letter, was a three word message that made his heart pound in his chest.

_Love, From M_


	2. Chapter 2

**A/N: So, here's the deal, I have been working on a science fiction book for five years and I recently got really into it. It kind of ate up all my time, but it's finished! Yay! All writing gremlins in my head now are back to obsessing over fanfiction, so the hiatus is over. Chapters will probably be coming more frequently now. Thank everyone!**

Ianto drove the dark van quickly through the dim streets with Gwen sitting tensely in the passenger seat, still holding the gun. Sherlock and John sat behind them in a thick silence.

John drummed his fingers against his thigh. "So…you work for MI6?"

Ianto shook his head. "No. We're outside of the government."

"_Beyond the police,"_ Sherlock muttered dramatically. "_Tracking down alien life on Earth, arming the human race against the future_."

"Hey!" Gwen said, pointing the gun warningly in John's direction.

Sherlock's arm darted forward and grabbed the gun, yanking it back across his lap. "First, do not point a gun at John or myself. Second, as I've explained, it's not a gun and you look like an idiot. Third, John knows about aliens, as do I. Do you honestly think Jack would send you to someone who didn't? Lastly, if you wish to help us, I suggest you calm down. Turn left up ahead."

"Who put you in charge?" Gwen asked.

"Jack. Are you not paying attention?"

"Exactly how do you know Jack?" Ianto asked.

"Here," Sherlock said, opening the door before the car stopped in front of a bustling building. Next to the building was a stairway into the underground.

"Sherlock!" John grumbled as Ianto slammed on the brakes.

"We need to move, John," he said simply.

He jogged to catch up with him, grabbing his arm. "Sherlock," he said quietly, "I'm sorry, I really am, but we have to prepare for the possibility that…" he faltered, dropping his eyes a bit. "I'm sorry, but if Moriarty is behind this and he took your friend that long ago…Sherlock he's probably dead."

Sherlock snorted. "Um, no. He's not. Well, he might be, but it's nothing to be concerned about."

John frowned. "What?"

Sherlock broke free, running down the stairs. They followed him, pushing past the busy late-night crowd.

"A bus?" Gwen asked skeptically. "We're taking a bus?"

"Oh God," Sherlock muttered. "Here I assume Jack sends me a crack team, and I get an idiot."

"Excuse me!" she spat. "I am an agent of Torchwood, and before that I was with the police."

"Detective?"

"Police Constable."

He sighed. "A Police Constable and a coffee boy."

"How did you know—"

"Jack likes his coffee," Sherlock said simply, stopping in his tracks and running his hands along a wall. The wall was covered in small boxes with keyholes, numbered in the hundreds.

"A deposit box?" Gwen asked skeptically. "I think the numbers a bit long for that."

"John," Sherlock said flippantly, "I've decided I'm not going to talk to PC Cooper anymore. She's slowing me down with stupid observations. However, if you were curious, my family has a special system to send important messages confidentially throughout London. The first two numbers of any string of numbers we send refers to the location of an underground station. The next three are the box number. The lock is constructed to match the key to the TARDIS, and we all have a key."

"That's only five numbers. There are seven more."

"I know," he mused, turning the key in the lock. He opened the box and sand began pouring out, piling onto the floor. He pulled out a small black contraption connected to a wrist band. "I suspect the rest are for this."

"That's Jack's!" Ianto said, taking it from his and turning it over.

Sherlock yanked it back. "Yes, I know, thank you Coffee Boy. It's a vortex manipulator."

"Sherlock—" John started, looking at Ianto apologetically.

"No," Sherlock cut him off, punching a series of numbers into the device. "I've had enough of teamwork. Plus, I'm rather impartial to people who _destroy my flat_. If you want Jack back, then get back there and replaced our door and our window. Also, John needs a new teacup."

"You have got to be kidding me," Gwen scoffed.

"Not at all," Sherlock said, strapping the thing to his wrist. "We don't need you anymore. You're not going to remember us anyway, so, bye," Sherlock grabbed ahold of John's arm and something clicked.

John gasped as the world dropped out from under him. Nothing made sense. Colors whirled around them. His mind bent into two dimensions and then back again. He felt his own feet hit the top of his head. The only thing he was certain of was Sherlock's tight grasp on his arm, but no matter how hard he called for him no sound came from his lips.

He gasped, suddenly seeing blue sky above him. He felt soft sand beneath his neck. Sherlock's hand was still on his arm, and he heard the other man gasping for air next to him. John took deep breaths, desperately trying to moisten his mouth.

"What was that?" he finally gasped out.

"Time travel. The hard way. You're a bit spoiled, you've only traveled in the TARDIS. It's like driving in a sports car your whole life and then being stuck in a bumper car. Time travel without a vessel is…unpleasant."

"It feels like I have a nasty hangover," John muttered as Sherlock helped him to his feet.

"Be glad we're only displaced by two weeks. I had to jump fifty years once. I passed out for three days."

John glanced around. They were on some empty beach, the calm waves lapping gently only yards away. He winced into the bright sunlight. "Two weeks? Oh, God, I won't be able to stand the return trip."

"There won't be one. We're changing the last two weeks to pick up Jack just after he was captured. We'll remember what happened because if we didn't we wouldn't know why we were here."

"We're disappearing for two weeks?" John balked. "Sherlock, I have a job, I can't just—"

"No, you don't understand. Whatever you did in the last two weeks, that all still happens. We are now living in a world with two John Watsons and two Sherlock Holmes. One pair is living peacefully at Baker Street, unaware of what is going on. The only difference is that the two of us will be saving Jack right away, so Torchwood will have no reason to contact us. At the end of two weeks the timelines will readjust, and we'll be one pair again that remembers everything. It'll be a bit annoying to have simultaneous memories, I have to warn you. I once accidently attended four separate cocktail parties at the same time."

"I'm lost," he mumbled. "Why are we on a beach?"

"These were the coordinates on the paper," he shrugged, covering his eyes and staring out across the sand. "Jack!" he called. They heard nothing.

They started out across the beach, calling his name. "Oh," John said suddenly, furrowing his eyebrows, "what did you need, by the way?"

"What?"

"Earlier before the…gun—hey, will our flat be a mess when we get back?"

Sherlock smirked. "No. They've never come to the flat. It'll be just as we left it."

"Beer and licorice," John smiled. "So before all that, what did you want to tell me?"

"Uh…nothing. It's not important, just odds and ends about a case."

"I thought there were no cases?"

Sherlock sighed, sliding his scarf off of his neck in the thick heat. Now was as good as ever.

"Hey!" a voice called from down the beach.

They jumped looking around desperately. There was no one in sight. "Jack!" Sherlock called out.

"Hey! Hurry up!"

They ran down the beach peering into the distance. "Jack!"

"Stop!" the voice ordered.

They froze. "Jack?"

"Over here," the voice said slightly to the right.

John gasped. A man was buried in the sand, only his head poking out from the deep hole. The tide had come in somewhat, and he had to spit water out of the hole to speak. He was gasping for air, trying desperately to turn his head to see the two men.

Sherlock smiled. "Jack."

"Hey, kid," Jack smiled, peering up from the sand. He glanced at John and the grin widened. "Hello to you, too. Captain Jack Harkness. I'd shake your hand, but I'm a little tied up at the moment."

"No," Sherlock said immediately, making harsh eye contact with Jack. "Don't do that."

Jack laughed. "Get me out of here. We need to talk."

"About what."

"Moriarty."


	3. Chapter 3

**A/N:Okay, I have a good reason this time. I fell on my laptop—really. It cracked the whole screen and had to be sent to a repair shop—all of my fanfics were unreachable for weeks it sucked. More to come **

Jack was late, and that wasn't right. Sure, he wasn't very late, but as Ianto Jones walked nervously around the main level of the hub the absence of the strange man hung heavily in the air. Gwen was tapping her foot softly, disguising her worried panic as a coffee break. Even Tosh, typing slowly and grumpily at the failing program ahead of her, seemed to slow down as she glanced nervously at the door.

The funny thing about a perception filter is that it works below ground as well as above. As the small slab of pavement lowered down into the center of the hub, not one of the nervous employees even glanced in their direction.

Sherlock snorted, glancing around the room. "They're looking for you, and they still can't see you. No wonder your team needs help, they're pathetic."

"Are we invisible?" John chuckled, staring at his own hands. He was staring in shock at the wide, cavernous halls around him. As usual, he saw a look of complete disinterest on Sherlock's face. Nothing was knew to him, nothing was novel.

"No. Not to anyone who's actually looking. Perception filters only make you want to look away. They can be useful. I've brought home three dead bodies in the last year, you didn't notice."

Ianto was standing quite close to the slab when Jack stepped off and appeared directly in front of him. He jumped, the coffee cup falling from his hands and landing with a harsh thump on the metal floor.

"Jack! I didn't realize you were here."

"I wasn't," Jack said, hopping down to peek at the slow program on Tosh's computer. "I was kidnapped."

"Kidnapped?" Gwen asked, squinting at the two strange men following Jack down to the screens.

"Not by us, PC Cooper," Sherlock sneered at her. "It's good to see you're as clever as ever."

"Do I know you?"

Jack chuckled. "How far are you displaced Sherlock? A week?"

"Two. Your Meter Maid and Coffee Boy came to your rescue by blowing up our flat."

"No, we didn't," Ianto frowned. "Jack, you're covered in sand."

"But they…would have?" John asked. "If Jack had been gone for two weeks?"

"Right," Sherlock nodded at him, smiling slightly. "I imagine Moriarty got bored of waiting and sent them the clue eventually."

"Moriarty is a person?" Jack asked.

Sherlock frowned. "Obviously. What did you think it was?"

"Not a clue," Jack said, turning the screen for him. There were small squiggles running across the screen, flipping and turning as the human made computer struggled with their complexity. John thought they looked a bit like runes, or perhaps the nonsensical letters a small child might try to pass off as a letter. Sherlock was peering at them, his head slightly tilted as brief comprehension crossed his face.

"This is High Gallifreyan," Sherlock mused. "Where did you get this?"

"Yesterday a letter arrived upstairs in our cover store, addressed to 'The Idiots Who Believe Their Base Is a Secret', Care of Jack Harkness. It was one page of these symbols, signed 'Moriarty'. I honestly thought that was some new race of Aliens we hadn't heard of, so we scanned the symbols into this translator. We acquired it from the Raxacoricophalapiturians last year as part of a peace treaty— it's supposed to be able to translate any language in less than an hour. It's been running for twenty-four hours straight, and it hasn't cracked a single letter."

"You might as well stop the program, it'll just overload it. Did you call my father?"

"I tried last night, just before…I can't remember what happened after that."

"Jack," Ianto said again, "why are you covered in sand?"

Jack smiled at him. "I'm okay, really. I wasn't there too long."

John saw something— just for a second—a small look exchanged between Jack and the panicked man behind him. His eyebrows raised for a second, not used to being the one making deductions. He wondered if Sherlock had noticed whatever was between them. Well, obviously, he supposed if he had noticed his flat-mate had already deduced their anniversary, ages, and differences in weight.

"Can you read it, Sherlock?" Jack asked, breaking through John's thoughts.

Sherlock frowned, squinting harder at the squiggles. He sighed in frustration rubbing at his forehead.

"Are you okay?" John asked as Sherlock winced.

"It's like…It's like reading a waterproof book at the bottom of a swimming pool in the sunlight. Technically possible, but really difficult, and it hurts my eyes. Have you tried calling Mycroft? He's more alien than me, he could probably read it better than I can."

"I called him first, he didn't answer."

Sherlock frowned. "And the Doctor didn't answer either?"

Jack shrugged. "That's not so unusual. They might always answer when you boys call, but the rest of the universe isn't so lucky."

Sherlock wasn't paying attention, already searching through the contacts in his mobile. He dialed and waited nearly a full minute, listening to the dull ringing on the other side of the line. No one answered.

"John, dial my parents."

John snorted, "Sherlock, if you can't get ahold of them then I certainly can't—hey!" he objected as Sherlock pulled his phone from his jacket and dialed a long number.

"Never once in my life has my mother not answered a phone call from my number. She was running from a Shifter once, answered me mid-sprint and told me to hold for a minute." He dialed Mycroft's number on his phone. "If they aren't answering, something is either stopping them or the signal."

Mycroft's line rang dully, echoing through the speaker in a suddenly quiet room. They all stared at the device and waited for someone to answer. There was a click as it moved to voicemail. The recording was silent for a moment, the faint sound of someone breathing on the other line. Finally, one voice came over the phone—one sing-song, familiar voice.

"Sherrrrr-looock," Moriarty called from the phone. The beep sounded immediately afterwards, but Sherlock had already tossed his phone to the ground, grabbing the computer screen and staring at it, fighting back against the aching in his skull.

John knew the look on his face, the quiet terror mixed with that sick sense of intellectual curiosity that infuriated him sometimes. "Sherlock," John asked cautiously, "what's going on?"

"Mycroft's in trouble, and my parents are being blocked from us somehow," he growled. "Two weeks—two weeks! How could I not have noticed what was happening right in front of me? God!" he winced, covering his eyes from the screen.

"Can you get any of it?" Ianto asked.

"I don't need advice from the Coffee Boy!" Sherlock snapped.

"Sherlock." Jack warned, calmly.

The younger man sighed, rubbing his face. "I'm sorry. That was Moriarty on Mycroft's voicemail. There's no telling how long he's had him. This message is our only clue. It hurts. It's a short message really. Something like…I see my name in it… time, I recognize that symbol. Raised? Moved? I can't make it out."

"Raised?" Toshiko asked, biting her lip.

"What? Who are you? Stop talking." Sherlock snapped.

"Time's raised…" she continued. "Time's…Up…Sherlock?"

The lights in the hub went out.


End file.
